By Rebecca Halpin

Influenza H1N1pdm sequencing project overview

Since 2004, the JCVI Influenza Genome Sequencing Project, funded by the National Institute of Allergy and Infectious Diseases (NIAID), has sequenced thousands of human, swine, and avian influenza isolates from collections around the world to provide researchers with a better understanding of the evolution of this important pathogen and to enable the development of new therapeutics, diagnostics, and vaccines.

JCVI has been collaborating with groups worldwide to monitor the evolution of the pandemic H1N1 Influenza virus (also known as H1N1pdm) that entered the human population in the spring of 2009 and has been responsible for at least 16,226 deaths worldwide. Genomic sequence information and epidemiological data are being used to address critical scientific questions of virus adaptation.

Some of the questions we are trying to answer with our current H1N1pdm studies include:

  • How do pandemic viruses collected during the first wave of the pandemic compare to those collected in the later phases? We have ongoing studies in New York, Texas, Wisconsin, and California which address this question.
  • How will the presence of a new pandemic influenza virus affect the evolution of seasonal H1N1 and H3N2 viruses? Will the seasonal viruses become extinct? Will we identify novel reassortants between the H1N1pdm and seasonal human viruses?
  • Will the pandemic virus acquire resistance to neuraminidase inhibitors such as Tamiflu?
  • How does H1N1pdm isolated in the tropics differ from isolates collected in temperate regions? What is the relationship between strains present in the tropics and epidemic strains in temperate regions? We have collections in Nicaragua, Hong Kong, and Brazil which will help answer these questions.
  • What are the evolutionary dynamics of H1N1pdm in a situation of intense viral transmission such as between students in a university setting?
  • Influenza samples have never been collected during the summer months. Thus the collection of pandemic influenza samples during the summer gives us a glimpse of viral persistence and transmission during the off peak months. How do circulating influenza strains collected during the southern hemisphere’s influenza season compare to those collected during the US summer and which strains persist into the next northern hemisphere flu season?

For more information please visit our project page.